deep substitution of implementations with interfaces

paolopavan · paolopavan · commit fc6352758ab5 · 2020-04-28T01:07:08.000+01:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/DatabaseReferenceInterface.java
@@ -24,6 +24,8 @@
 
 import java.util.ArrayList;
 import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
 
 /**
  * If a SequenceProxyReader implements this interface then that external source
@@ -32,5 +34,5 @@
  */
 public interface DatabaseReferenceInterface {
 
-	public LinkedHashMap<String,ArrayList<DBReferenceInfo>> getDatabaseReferences();
+	public Map<String, List<DBReferenceInfo>> getDatabaseReferences();
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureRetriever.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeatureRetriever.java
@@ -22,13 +22,14 @@
 
 package org.biojava.nbio.core.sequence.features;
 
-import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
 /**
  * If a SequenceProxyReader implements this interface then that external source
  * has a list features
  * @author @author Paolo Pavan
  */
 public interface FeatureRetriever {
-	HashMap<String, ArrayList<AbstractFeature>> getFeatures();
+	Map<String, List<AbstractFeature>> getFeatures();
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/features/FeaturesKeyWordInterface.java
@@ -22,7 +22,7 @@
 
 package org.biojava.nbio.core.sequence.features;
 
-import java.util.ArrayList;
+import java.util.List;
 
 /**
  * Models the keywords that are annotated for a protein sequence at Uniprot. If a ProxySequenceReader
@@ -36,5 +36,5 @@ public interface FeaturesKeyWordInterface {
 	 *
 	 * @return
 	 */
-	public ArrayList<String> getKeyWords() ;
+	public List<String> getKeyWords() ;
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankReader.java
@@ -170,7 +170,7 @@ public LinkedHashMap<String,S> process(final int max) throws IOException, Compou
 			.forEach(sequence::addFeature);
 
 			// add taxonomy ID to new sequence
-			ArrayList<DBReferenceInfo> dbQualifier = genbankParser.getDatabaseReferences().get("db_xref");
+			List<DBReferenceInfo> dbQualifier = genbankParser.getDatabaseReferences().get("db_xref");
 			if (dbQualifier != null){
 				DBReferenceInfo q = dbQualifier.get(0);
 				sequence.setTaxonomy(new TaxonomyID(q.getDatabase()+":"+q.getId(), DataSource.GENBANK));
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/GenbankSequenceParser.java
@@ -62,13 +62,13 @@ public class GenbankSequenceParser<S extends AbstractSequence<C>, C extends Comp
 	private String header;
 	private String accession;
 	private boolean isCircularSequence;
-	public Map<String, ArrayList<DBReferenceInfo>> mapDB;
+	private Map<String, List<DBReferenceInfo>> mapDB;
 	/**
 	 * this data structure collects list of features extracted from the
 	 * FEATURE_TAG section They are organized by list of the same type (i.e.
 	 * same genbank Feature) and are provided with location
 	 */
-	private HashMap<String, ArrayList<AbstractFeature>> featureCollection;
+	private HashMap<String, List<AbstractFeature>> featureCollection;
 
 	private final Logger log = LoggerFactory.getLogger(getClass());
 
@@ -430,7 +430,7 @@ public GenericGenbankHeaderParser<S, C> getSequenceHeaderParser() {
 		return headerParser;
 	}
 
-	public Map<String, ArrayList<DBReferenceInfo>> getDatabaseReferences() {
+	public Map<String, List<DBReferenceInfo>> getDatabaseReferences() {
 		return mapDB;
 	}
 
@@ -441,7 +441,7 @@ public List<String> getKeyWords() {
 	public List<AbstractFeature> getFeatures(String keyword) {
 		return featureCollection.get(keyword);
 	}
-	public Map<String, ArrayList<AbstractFeature>> getFeatures() {
+	public Map<String, List<AbstractFeature>> getFeatures() {
 		return featureCollection;
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReader.java
@@ -55,9 +55,7 @@
 import java.io.InputStreamReader;
 import java.net.URL;
 import java.net.URLConnection;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
+import java.util.*;
 
 /**
  * @author Karl Nicholas <github:karlnicholas>
@@ -72,7 +70,7 @@ public class GenbankProxySequenceReader<C extends Compound> extends StringProxyS
 	private GenbankSequenceParser<AbstractSequence<C>, C> genbankParser;
 	private GenericGenbankHeaderParser<AbstractSequence<C>, C> headerParser;
 	private String header;
-	private HashMap<String, ArrayList<AbstractFeature>> features;
+	private Map<String, List<AbstractFeature>> features;
 
 
 	/**
@@ -182,17 +180,17 @@ public GenericGenbankHeaderParser<AbstractSequence<C>, C> getHeaderParser() {
 		return headerParser;
 	}
 	@Override
-	public HashMap<String, ArrayList<AbstractFeature>> getFeatures() {
+	public Map<String, List<AbstractFeature>> getFeatures() {
 		return features;
 	}
 
 	@Override
-	public LinkedHashMap<String, ArrayList<DBReferenceInfo>> getDatabaseReferences() {
+	public Map<String, List<DBReferenceInfo>> getDatabaseReferences() {
 		return genbankParser.getDatabaseReferences();
 	}
 
 	@Override
-	public ArrayList<String> getKeyWords() {
+	public List<String> getKeyWords() {
 		return genbankParser.getKeyWords();
 	}
 
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
@@ -50,10 +50,7 @@
 import java.net.HttpURLConnection;
 import java.net.URL;
 import java.rmi.RemoteException;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
+import java.util.*;
 import java.util.regex.Pattern;
 
 /**
@@ -816,8 +813,8 @@ public ArrayList<String> getKeyWords() {
 	 * @return
 	 */
 	@Override
-	public LinkedHashMap<String, ArrayList<DBReferenceInfo>> getDatabaseReferences()  {
-		LinkedHashMap<String, ArrayList<DBReferenceInfo>> databaseReferencesHashMap = new LinkedHashMap<String, ArrayList<DBReferenceInfo>>();
+	public Map<String, List<DBReferenceInfo>> getDatabaseReferences()  {
+		Map<String, List<DBReferenceInfo>> databaseReferencesHashMap = new LinkedHashMap<>();
 		if (uniprotDoc == null) {
 			return databaseReferencesHashMap;
 		}
@@ -829,7 +826,7 @@ public LinkedHashMap<String, ArrayList<DBReferenceInfo>> getDatabaseReferences()
 			for (Element element : dbreferenceElementList) {
 				String type = element.getAttribute("type");
 				String id = element.getAttribute("id");
-				ArrayList<DBReferenceInfo> idlist = databaseReferencesHashMap.get(type);
+				List<DBReferenceInfo> idlist = databaseReferencesHashMap.get(type);
 				if (idlist == null) {
 					idlist = new ArrayList<DBReferenceInfo>();
 					databaseReferencesHashMap.put(type, idlist);
@@ -846,7 +843,7 @@ public LinkedHashMap<String, ArrayList<DBReferenceInfo>> getDatabaseReferences()
 			}
 		} catch (XPathExpressionException e) {
 			logger.error("Problems while parsing db references in UniProt XML: {}. No db references will be available.",e.getMessage());
-			return new LinkedHashMap<String, ArrayList<DBReferenceInfo>>();
+			return new LinkedHashMap<>();
 		}
 
 		return databaseReferencesHashMap;
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
@@ -126,7 +126,7 @@ public void setProxySequenceReader(SequenceReader<C> proxyLoader) {
 
 		if (proxyLoader instanceof FeatureRetriever) {
 			this.setFeatureRetriever((FeatureRetriever) sequenceStorage);
-			HashMap<String, ArrayList<AbstractFeature>> ff = getFeatureRetriever().getFeatures();
+			Map<String, List<AbstractFeature>> ff = getFeatureRetriever().getFeatures();
 			for (String k: ff.keySet()){
 				for (AbstractFeature f: ff.get(k)){
 					this.addFeature(f);
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
@@ -45,6 +45,7 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
+import java.util.List;
 
 /**
  * Testing example for issue #834
@@ -187,7 +188,7 @@ public void testProteinSequenceFactoring() throws Exception {
 		ProteinSequence seq = new ProteinSequence(genbankReader);
 
 		// if target protein contain CDS/coded_by than it should contain parent nucleotide seq
-		ArrayList<AbstractFeature> CDSs = genbankReader.getFeatures().get("CDS");
+		List<AbstractFeature> CDSs = genbankReader.getFeatures().get("CDS");
 
 		if (CDSs != null) {
 			if (CDSs.size() == 1) {

Original file line number	Diff line number	Diff line change
`@@ -22,7 +22,7 @@`
`22`	`22`
`23`	`23`	`package org.biojava.nbio.core.sequence.features;`
`24`	`24`
`25`		`-import java.util.ArrayList;`
	`25`	`+import java.util.List;`
`26`	`26`
`27`	`27`	`/**`
`28`	`28`	`* Models the keywords that are annotated for a protein sequence at Uniprot. If a ProxySequenceReader`
`@@ -36,5 +36,5 @@ public interface FeaturesKeyWordInterface {`
`36`	`36`	`*`
`37`	`37`	`* @return`
`38`	`38`	`*/`
`39`		`- public ArrayList<String> getKeyWords() ;`
	`39`	`+ public List<String> getKeyWords() ;`
`40`	`40`	`}`